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        <a href="moltk-module.html">Package&nbsp;moltk</a> ::
        Class&nbsp;Alignment
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Alignment</h1><p class="nomargin-top"></p>
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<p>Alignment represents a set of aligned macromolecule sequences and/or 
  structures.</p>

<!-- ==================== NESTED CLASSES ==================== -->
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      Meta-data for one sequence in an Alignment
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<!-- ==================== INSTANCE METHODS ==================== -->
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          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      __init__( (object)arg1) -&gt; None :</td>
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          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#__reduce__" class="summary-sig-name">__reduce__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      helper for pickle</td>
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      <span class="summary-type">&nbsp;</span>
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          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      __str__( (Alignment)arg1) -&gt; object :</td>
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          </td>
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      <span class="summary-type">&nbsp;</span>
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          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#align" class="summary-sig-name">align</a>(<span class="summary-sig-arg">...</span>)</span><br />
      align( (Alignment)arg1, (Alignment)arg0, (EString)arg1, (EString)arg2) -&gt; Alignment :</td>
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          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#append_sequence" class="summary-sig-name">append_sequence</a>(<span class="summary-sig-arg">...</span>)</span><br />
      append_sequence( (Alignment)arg1, (Biosequence)sequence) -&gt; Alignment :</td>
          <td align="right" valign="top">
            
            
          </td>
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      </table>
      
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
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        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#fasta" class="summary-sig-name">fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      fasta( (Alignment)arg1) -&gt; str :</td>
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      <span class="summary-type">&nbsp;</span>
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          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#get_estring" class="summary-sig-name">get_estring</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_estring( (Alignment)arg1, (int)index) -&gt; EString :</td>
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          </td>
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        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#get_number_of_columns" class="summary-sig-name">get_number_of_columns</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_number_of_columns( (Alignment)arg1) -&gt; int :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#get_number_of_sequences" class="summary-sig-name">get_number_of_sequences</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_number_of_sequences( (Alignment)arg1) -&gt; int :</td>
          <td align="right" valign="top">
            
            
          </td>
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      </table>
      
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      <span class="summary-type">&nbsp;</span>
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      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#get_sequence" class="summary-sig-name">get_sequence</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_sequence( (Alignment)arg1, (int)index) -&gt; BaseBiosequence :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#id_table" class="summary-sig-name">id_table</a>(<span class="summary-sig-arg">...</span>)</span><br />
      id_table( (Alignment)arg1) -&gt; str :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#load_fasta" class="summary-sig-name">load_fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      load_fasta( (Alignment)arg1, (object)input_stream) -&gt; Alignment :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#load_string" class="summary-sig-name">load_string</a>(<span class="summary-sig-arg">...</span>)</span><br />
      load_string( (Alignment)arg1, (str)alignment_string) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#pretty" class="summary-sig-name">pretty</a>(<span class="summary-sig-arg">...</span>)</span><br />
      pretty( (Alignment)arg1) -&gt; str :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#score" class="summary-sig-name">score</a>(<span class="summary-sig-arg">...</span>)</span><br />
      score( (Alignment)arg1) -&gt; Information :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#set_score" class="summary-sig-name">set_score</a>(<span class="summary-sig-arg">...</span>)</span><br />
      set_score( (Alignment)arg1, (Information)s) -&gt; Alignment :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#write_fasta" class="summary-sig-name">write_fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      write_fasta( (Alignment)arg1, (object)output_stream) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#write_id_table" class="summary-sig-name">write_id_table</a>(<span class="summary-sig-arg">...</span>)</span><br />
      write_id_table( (Alignment)arg1, (object)output_stream) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Alignment-class.html#write_pretty" class="summary-sig-name">write_pretty</a>(<span class="summary-sig-arg">...</span>)</span><br />
      write_pretty( (Alignment)arg1, (object)output_stream) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
  <tr>
    <td colspan="2" class="summary">
    <p class="indent-wrapped-lines"><b>Inherited from <code><i>unreachable</i>.instance</code></b>:
      <code>__new__</code>
      </p>
    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
      <code>__delattr__</code>,
      <code>__format__</code>,
      <code>__getattribute__</code>,
      <code>__hash__</code>,
      <code>__reduce_ex__</code>,
      <code>__repr__</code>,
      <code>__setattr__</code>,
      <code>__sizeof__</code>,
      <code>__subclasshook__</code>
      </p>
    </td>
  </tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Class Variables</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-ClassVariables"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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  </td>
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<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="LIST_SEQUENCE"></a><span class="summary-name">LIST_SEQUENCE</span> = <code title="moltk._moltk.List.LIST_SEQUENCE">moltk._moltk.List.LIST_SEQUENCE</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="LIST_STRUCTURE"></a><span class="summary-name">LIST_STRUCTURE</span> = <code title="moltk._moltk.List.LIST_STRUCTURE">moltk._moltk.List.LIST_STRUCTURE</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="__instance_size__"></a><span class="summary-name">__instance_size__</span> = <code title="96">96</code>
    </td>
  </tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
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         ><span class="options">[<a href="#section-Properties"
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         >hide private</a>]</span></td>
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    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
      <code>__class__</code>
      </p>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
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<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">...</span>)</span>
    <br /><em class="fname">(Constructor)</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

__init__( (object)arg1) -&gt; None :

    C++ signature :
        void __init__(struct _object *)

__init__( (object)arg1, (Biosequence)sequence) -&gt; None :

    C++ signature :
        void __init__(struct _object *,class moltk::Biosequence)

__init__( (object)arg1, (str)alignment_string) -&gt; None :

    C++ signature :
        void __init__(struct _object *,class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

__init__( (object)arg1, (str)alignment_string) -&gt; None :

    C++ signature :
        void __init__(struct _object *,char const *)

</pre>
  <dl class="fields">
    <dt>Overrides:
        object.__init__
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="__reduce__"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__reduce__</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <p>helper for pickle</p>
  <dl class="fields">
    <dt>Overrides:
        object.__reduce__
        <dd><em class="note">(inherited documentation)</em></dd>
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">...</span>)</span>
    <br /><em class="fname">(Informal representation operator)</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

__str__( (Alignment)arg1) -&gt; object :

    C++ signature :
        struct _object * __str__(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
    <dt>Overrides:
        object.__str__
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="align"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">align</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

align( (Alignment)arg1, (Alignment)arg0, (EString)arg1, (EString)arg2) -&gt; Alignment :

    C++ signature :
        class moltk::Alignment align(class moltk::Alignment {lvalue},class moltk::Alignment,class moltk::EString,class moltk::EString)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="append_sequence"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">append_sequence</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

append_sequence( (Alignment)arg1, (Biosequence)sequence) -&gt; Alignment :

    C++ signature :
        class moltk::Alignment {lvalue} append_sequence(class moltk::Alignment {lvalue},class moltk::Biosequence)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

fasta( (Alignment)arg1) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; fasta(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_estring"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_estring</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_estring( (Alignment)arg1, (int)index) -&gt; EString :

    C++ signature :
        class moltk::EString get_estring(class moltk::Alignment {lvalue},unsigned int)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_number_of_columns"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_number_of_columns</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_number_of_columns( (Alignment)arg1) -&gt; int :

    C++ signature :
        unsigned int get_number_of_columns(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_number_of_sequences"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_number_of_sequences</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_number_of_sequences( (Alignment)arg1) -&gt; int :

    C++ signature :
        unsigned int get_number_of_sequences(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_sequence"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_sequence</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_sequence( (Alignment)arg1, (int)index) -&gt; BaseBiosequence :

    C++ signature :
        class moltk::BaseBiosequence get_sequence(class moltk::Alignment {lvalue},unsigned int)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="id_table"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">id_table</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

id_table( (Alignment)arg1) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; id_table(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="load_fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">load_fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

load_fasta( (Alignment)arg1, (object)input_stream) -&gt; Alignment :

    C++ signature :
        class moltk::Alignment {lvalue} load_fasta(class moltk::Alignment {lvalue},class std::basic_istream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

load_fasta( (Alignment)arg1, (str)file_name) -&gt; Alignment :

    C++ signature :
        class moltk::Alignment {lvalue} load_fasta(class moltk::Alignment {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="load_string"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">load_string</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

load_string( (Alignment)arg1, (str)alignment_string) -&gt; None :

    C++ signature :
        void load_string(class moltk::Alignment {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="pretty"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">pretty</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

pretty( (Alignment)arg1) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; pretty(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="score"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">score</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

score( (Alignment)arg1) -&gt; Information :

    C++ signature :
        struct moltk::units::Quantity&lt;struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,0,1&gt; &gt;,double&gt; score(class moltk::Alignment {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="set_score"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">set_score</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

set_score( (Alignment)arg1, (Information)s) -&gt; Alignment :

    C++ signature :
        class moltk::Alignment {lvalue} set_score(class moltk::Alignment {lvalue},struct moltk::units::Quantity&lt;struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,0,1&gt; &gt;,double&gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="write_fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">write_fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

write_fasta( (Alignment)arg1, (object)output_stream) -&gt; None :

    C++ signature :
        void write_fasta(class moltk::Alignment {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

write_fasta( (Alignment)arg1, (str)file_name) -&gt; None :

    C++ signature :
        void write_fasta(class moltk::Alignment {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="write_id_table"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">write_id_table</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

write_id_table( (Alignment)arg1, (object)output_stream) -&gt; None :

    C++ signature :
        void write_id_table(class moltk::Alignment {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

write_id_table( (Alignment)arg1, (str)file_name) -&gt; None :

    C++ signature :
        void write_id_table(class moltk::Alignment {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="write_pretty"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">write_pretty</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

write_pretty( (Alignment)arg1, (object)output_stream) -&gt; None :

    C++ signature :
        void write_pretty(class moltk::Alignment {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

write_pretty( (Alignment)arg1, (str)file_name) -&gt; None :

    C++ signature :
        void write_pretty(class moltk::Alignment {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
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